› 7cy4

X-ray diffraction
2.2Å resolution

Crystal Structure of CMD1 in apo form

Released:
DOI: 10.2210/pdb7cy4/pdb
Model geometry
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PDB entry 7cy4 coloured by chain, front view.
PDB entry 7cy4 coloured by chain, side view.
PDB entry 7cy4 coloured by chain, top view.
Source organisms:
Primary publication:
Molecular mechanism for vitamin C-derived C5-glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1.
Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding J
OpenAccess logo Nat Commun 12 744 (2021)
PMID: 33531488

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-104296 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5-methylcytosine-modifying enzyme 1; Maltose/maltodextrin-binding periplasmic protein Chain: A
Molecule details ›
Chain: A
Length: 917 amino acids
Theoretical weight: 98.91 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AEX9 (Residues: 27-392; Coverage: 99%)
  • Canonical: A0A2K3D5Z7 (Residues: 1-532; Coverage: 100%)
Gene names: CHLRE_12g553400v5, CMD1, JW3994, b4034, malE
Sequence domains: Bacterial extracellular solute-binding protein

Ligands and Environments

2 bound ligands:
Ligand FE 1 x FE
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 154.677Å b: 123.573Å c: 64.206Å
α: 90° β: 103.16° γ: 90°
R-values:
R R work R free
0.182 0.18 0.223
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Multiple Physiological and Biochemical Functions of Ascorbic Acid in Plant Growth, Development, and Abiotic Stress Response.
Wu et al. (2024)
2 other articles

1 mention without citation

Molecular mechanism for vitamin C-derived C5-glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1.
Li et al. (2021)

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